User: user230613

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user230613240
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2 years, 11 months ago
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Posts by user230613

<prev • 57 results • page 1 of 6 • next >
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Comment: C: Specific sequence abundance using RNA-Seq
... @Brian, I want to measure the expression of that sequence using RNA-Seq data, I don't want to extract the Kmer sequence from my reads. ...
written 12 weeks ago by user230613240
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Specific sequence abundance using RNA-Seq
... Hi, I would like to measure the expression, the abundance, of a given sequence, a specific 9-mer. I have `RNA-Seq` data. I know that the 9-mer is not unique in the genome, is not private of a specific gene. It is present in more than one isoform of gene A and also is present in gene B. How can I ge ...
expression rna-seq written 12 weeks ago by user230613240 • updated 12 weeks ago by Brian Bushnell14k
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Comment: C: What Ngs Read Simulators Are Available For Paired-End Data?
... Thank you for the fast answer. I'll try the bedtools pre-step. Another issue.. I've realised that in PE mode, the names of the output reads in the two files are not paired, is there any option for this? ...
written 3 months ago by user230613240
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Comment: C: What Ngs Read Simulators Are Available For Paired-End Data?
... Hi Brian! Is it possible to generate reads in specific intervals? WES-like read simulation? ...
written 3 months ago by user230613240
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Comment: C: Subset of transcripts - Do I need to re-scale the TPM values?
... Mmmm.. that's true, but I'm not interested in the non-coding transcripts at all. That's why I have posted a second question "Is there a difference between this approach or running Kallisto only on those coding transcripts?", because if you use only coding set of transcripts when running kallisto, th ...
written 3 months ago by user230613240
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Subset of transcripts - Do I need to re-scale the TPM values?
... Hi! Apologies in advance if this question is very basic =) I have run `Kallisto` using the full human transcriptome dataset `GRCh37-75`. This dataset includes both coding and non-coding transcripts, obviously. I would like to further analyse the coding ones. Since the `TPM` measurement take into a ...
tpm kallisto rna-seq written 3 months ago by user230613240
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TPM VS FPKM VS TMM and K-mer specific expression quantification
... Hi Biostar's! I'm trying to find the best approach to fill my goal. I would like to measure the expression of specific set of kmers - 10 aa long peptide sequences across different samples. I have RNA-Seq data for each sample. I'm planing to use alignment-independent methods such as `Kallisto` or `S ...
kmer rna-seq written 3 months ago by user230613240 • updated 7 weeks ago by Rob2.0k
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Comment: C: kallisto: strand-specific and fragment length calculation
... Sorry, I have another question, "fragment-length" is not the same as read length, is it? I mean, it can't be inferred using input SE fastq files ...
written 4 months ago by user230613240
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kallisto: strand-specific and fragment length calculation
... Hi! I'm starting to use kallisto to do transcript-level expression quantification. I have some questions: **1)** Does `kallisto` infer the strandness of the input data just like `salmon` does (`--libType A`)? I guess the answer is no. **2)** For other hand, `kallisto` has the next to options: ...
kallisto rna-seq written 4 months ago by user230613240 • updated 4 months ago by pmelsted50
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Comment: C: bam-readcount tool: output zero coverage bases
... You're right. My mistake :/ ...
written 5 months ago by user230613240

Latest awards to user230613

Popular Question 11 weeks ago, created a question with more than 1,000 views. For promoter position estimation
Popular Question 11 weeks ago, created a question with more than 1,000 views. For CIRCOS plot with Chip-Seq Data
Popular Question 4 months ago, created a question with more than 1,000 views. For Intersect multiple bed and keep all fields
Student 4 months ago, asked a question with at least 3 up-votes. For Extract reads within given region, and their mates
Popular Question 8 months ago, created a question with more than 1,000 views. For Trinity strand specific: RF or FR
Popular Question 10 months ago, created a question with more than 1,000 views. For Trinity strand specific: RF or FR
Popular Question 10 months ago, created a question with more than 1,000 views. For Intersect multiple bed and keep all fields
Popular Question 15 months ago, created a question with more than 1,000 views. For Trinity strand specific: RF or FR
Popular Question 15 months ago, created a question with more than 1,000 views. For Extract sequence number "X" from multifasta file
Popular Question 15 months ago, created a question with more than 1,000 views. For Extract reads within given region, and their mates
Supporter 2.4 years ago, voted at least 25 times.

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